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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTGAGAAACAAGGACGTCGACTACGTGCTTGTTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAGgtatgttttcttgcgcgcagtttgtgtggcgtgtgacttatgtcagtcgtatggtggctggcgttgctcccgcag

Basic information

species Selaginella moellendorffii
transcript EFJ23417
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23417 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 5'ss of exon 5
GATGTGAGAAACAAGGACGTCGACTACGTGCTTGTTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAGgtatgttttcttgcgcgcagtttgtgtggcgtgtgacttatgtcagtcgtatggtgg--ctggcgttgctcccgcag-------
||||  | |   || ||| ||||  | |||||  |||| || |||||||| ||||||||||||||||||||||||||||| ||||||  | |   | |   ||   | | | |    || ||  |   ||| ||||  | |   ||   |||      ||        
GATGCCAAAGCTAAAGACATCGATGATGTGCTGATTCTTTCTGGTGATCATCTCTACCGCATGGACTACATGGACTTTGTTCAGgtaattgtctgtacatacatcatttcttgtagttggctgttaa-agtagtatatttgaattgattttgggtatccaatttacag

upper sequence: EFJ23417 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GRMZM2G391936_T03 (Zea mays), 5'ss of exon 5
GATGTGAGAAACAAGGACGTCGACTACGTGCTTGTTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAGgtatgttt--tcttgcgcgcagtttgtgtggcgtgtgacttatgtcagtcgtatggtggctggcgttgctcccgcag
||||  | |   || ||| | ||  | |||||  |||| || ||||| || |||||||| |||||||||||||||||||| ||||||   |   | || |  | ||  ||| |    |||     || |   |  | |  | |      || | |  ||||
GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaattttcccggtaggctgttta---tgtagtacatattgatttttttttcg-----atttcacttgcag

upper sequence: EFJ23417 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GLYMA07G38820.1 (Glycine max), 5'ss of exon 5
GATGTGAGAAACAAGGACGTCGACTACGTGCTTGTTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAGgtatgttttcttgcgcgcagtttgtgtggcgtgtgacttatgtcagtcgtatggtg-gctggcgttgct--cccgcag--------------------------
|||   ||||  |||||  | ||  | ||  |  |||| ||||| |||||||||||||| |||||||| ||||||||||| || ||| |      |||   |   |              |   |   | ||   || ||   |    ||| |  | | |||                          
GATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCCGGGGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAAgtaaggcactgtgccatccaatcaaacaattctcccccctttcaattcagttgatgcattcaaattgttgactctcagatgttttgactccttttcatatccag

upper sequence: EFJ23417 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GLYMA17G01900.1 (Glycine max), 5'ss of exon 5
GATGTGAGAAACAAGGACGTCGACTACGTGCTTGTTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAGgtatgttttcttgcgcgcagtttgtgtggcgtgtgacttatgtcagtcgtatggtggc--tggcgttgct--cccgcag--------------------------
|||   ||||  |||||  | ||  | ||  |  |||| || || |||||||||||||| |||||||| ||||||||||| || ||| |      |||   |   |    |         |   | |||||    | |   |  |    ||| |  | | |||                          
GATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCTGGAGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAAgtaaggcactgtgccatccaatcaaataattctctccccctttcagtttagttgatacattcaaattgttgactctcagatgttttgactcattttcatatccag

upper sequence: EFJ23417 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: PP1S347_12V6.1 (Physcomitrella patens), 5'ss of exon 5
--------------------------------------GATGTGAGAAACAAGGACGTCGACTACGTGCTTGTTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAGgtatgttttcttgcgcgcagtttgtgtggcgtgtgactta-tgtcagtcgtatggtggctggcgttgctcccgcag----
                                      |    ||   ||| ||||   |    ||   |     | ||  | |  | | |  ||  || | | |   ||||       ||   |   ||||   |    | ||    ||  |   |||||  | ||    || |  |  | |   | |   | | ||    
CCGGCGATCACCTCTACCGTATGGATTACATGGACTTTGTCCAGAAGCACAGGGACAGTGGTGCCGATATCACAATATCTTGCGTGCCCATGGACGACAGgtattcagtggaaccacaacatccagaatttccgtctgagaattcac-tgctgatggacttggtttctacagtttacttacagat-tagtgactgtagtatt

upper sequence: EFJ23417 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: PP1S2_204V6.1 (Physcomitrella patens), 5'ss of exon 4
GATGTGAGAAACAAGGACGTCGACTACGTGCTTGTTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAGgtatgttttcttgcgcgcagtttgt-gtggcgtgtgacttatgtcagtcg-tatg-gtggctggcgttgctcccgcag-------------------------------------------------------------------------------------------------------------------
|||| ||  || || |  || ||  ||||  |  |  | ||||| ||||| || || || |||||||||||||||||||||||||||    | |   |   |  ||    ||  | | |     |  |   ||  |||| |  ||| |  || |  | |                                                                                                                      
GATGCGAAGAATAAAGTTGTAGAGGACGTTGTAATCTTGTCCGGAGATCATCTTTATCGTATGGACTACATGGACTTTGTCCAGgtaaacctccaaccttacgtttgaccgtctcctattttcaacatttttcaatatgtgctgctcgattttcaacagagatgtcaatgctcaagtgattggttactaggtcctaggattccggaattatggccgaggccaagatgatggctaactacaggaattctgatattgttttgtttttttcatataatag

upper sequence: EFJ23417 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: PP1S389_5V6.1 (Physcomitrella patens), 5'ss of exon 4
GATGTGAGAAACAAGGACGTCGACTACGTGCTTGTTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAGgtatgttttcttgcgcgcagtttgtgtggcgtgtgacttatgtcagtcgtatgg-tggctggcgttgctc-ccgcag------------------------------------------------------------------------------------------------------
||||  |  || ||||  || ||  ||||  |  || | ||||| || ||  | ||||| |||||||||||||||||||| ||||||  |  ||   | ||   |   | | |  ||| | | |  |||    ||    |  ||   |||| || ||||                                                                                                        
GATGCCAAGAATAAGGTTGTGGAAGACGTAGTAATTTTATCCGGAGACCATTTGTACCGTATGGACTACATGGACTTTGTTCAGgtaaatcctcagtcccgtgttcaattttgt-tgtcattgaactcatagctacaaataactctggttgttcaccgctagtcatctgaatttgtactcaagttttttcaaatgaagatctcaagaggcgtgtgatttggtagcaaggttcctcacagtgtcttgttttacgcatttgacag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|169065580|gb|FE474833.1|FE474833
EST:     TTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAG                         AAGCACAAGGACTCTGGTGCAGACATCACCATCTCATGTGTTCCTGTGGAC
genomic: TTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAGgtatgttttc ... gctcccgcagAAGCACAAGGACTCTGGTGCAGACATCACCATCTCATGTGTTCCTGTGGAC
EST: gi|169040801|gb|FE447852.1|FE447852
EST:     TTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAG                         AAGCACAAGGACTCTGGTGCAGACATCACCATCTCATGTGTTCCTGTGGAC
genomic: TTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAGgtatgttttc ... gctcccgcagAAGCACAAGGACTCTGGTGCAGACATCACCATCTCATGTGTTCCTGTGGAC
EST: gi|169034359|gb|FE443132.1|FE443132
EST:     TTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAG                         AAGCACAAGGACTCTGGTGCAGACATCACCATCTCATGTGTTCCTGTGGAC
genomic: TTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAGgtatgttttc ... gctcccgcagAAGCACAAGGACTCTGGTGCAGACATCACCATCTCATGTGTTCCTGTGGAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 9

GATGTGAGAAACAAGGACGTCGACTACGTGCTTGTTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAGgtatgttttc ... gctcccgcagAAGCACAAGGACTCTGGTGCAGACATCACCATCTCATGTGTTCCTGTGGACGAGAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGTGAGAAACAAGGACGTCGACTACGTGCTTGTTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAGgtatgttttcttgcgcgcagtttgtgtggcgtgtgacttatgtcagtcgtatggtggctggcgttgctcccgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA